--- Log opened Fri Mar 02 00:00:33 2012
00:01 < joshcryer> Cool
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00:41 < foucist> Steel_: so what's your transhumanism forum gonna be about..  i mean, if it's too general, your aunt might not be interested
00:41 < foucist> also, is it active etc?
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00:51 < Steel_> foucist, pms
01:06 < delinquentme> go!
01:15 < Steel_> hey dm
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01:15 < Steel_> sup
01:22 < delinquentme> howdah :D
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02:43 < ybit> http://www.youtube.com/watch?v=wbqC8zm7Hyg
02:43 < ybit> Open Source Ecology - Enterprise Plan
02:44 < ybit> i didn't know there was a plan to hire programmers to write cad/cam software
02:44 < ybit> ..and there's plan to pay 1.2million dollars for this
02:47 < ybit> eww: http://www.kickstarter.com/projects/373493158/open-hardware-needs-a-sourceforge-of-its-own
02:49 < ybit> http://www.youtube.com/watch?v=fMmP_85yOWk
02:49 < ybit> ose Open source CAD/CAM Solution
02:53 < ybit> i.e. an interview with this guy: http://opensourceecology.org/wiki/Mike_Apostol
02:57 < joshcryer> They stole my idea. Hopefully they're successful.
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03:10 < ybit> discussion on freecad forum: http://sourceforge.net/apps/phpbb/free-cad/viewtopic.php?f=8&t=2313
03:10 < ybit> http://forum.opensourceecology.org/discussion/623/freecad
03:10 < ybit> on ose forum
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04:36 < utopiah> 403 http://hplusmagazine.com
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06:33 < kanzure> utopiah: nie
06:33 < kanzure> *nice
06:37 < chris_99> yay, i just got transducers today to play with sonoluminescence
06:37 < kanzure> ybit: so they've hired someone to work on freecad?
06:45 < kanzure> why not hire juergen o__o
06:45 < kanzure> since he- you know- wrote freecad
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07:22 < AlonzoTG> yeah, that's an interesting phenomenon, I haven't seen it myself but it is probably one of the most tantalizing scientific mysteries still open.
07:28 < kanzure> what?
07:29 < AlonzoTG> sonoluminescence
07:30 < ThomasEgi> light-on-sound?
07:30 < kanzure> light-generated sound
07:30 < kanzure> and sometimes sound-generated light
07:31 < AlonzoTG> I suggest you look it up, it's quite cool, it was even featured in a Keanu Reeves movie. =P
07:31 < AlonzoTG> ... does your work for you... grumble grumble:
07:31 < kanzure> the epitome of cool.
07:31 < AlonzoTG> http://en.wikipedia.org/wiki/Sonoluminescence
07:33 < AlonzoTG> << was responding to Christ who spoke at 9:35 AM.
07:33 < AlonzoTG> er, chris,
07:34 < AlonzoTG> << is quite sick today, taking basically my third sick day this week....
07:35 < kanzure> "sick days" are for people who work
07:36 < AlonzoTG> Quite true.
07:36 < AlonzoTG> I've been trying heroically to save a doomed project for the HUD.
07:36 < AlonzoTG> the DGRS.
07:36 < AlonzoTG> =P
07:36 < AlonzoTG> Some of the screens take 2 minutes to load! =P
07:37 < AlonzoTG> and the code is basically unmaintained,
07:37 < AlonzoTG> they just try to add new features without "breaking it"
07:37 < AlonzoTG> without trying to seriously overhaul and modernize it.
07:40 < AlonzoTG> after working on it for like two weeks, Netbeans counts 1,300 errors and 13,000 other defects.
07:40 < chris_99> sorry was afk, AlonzoTG i'm just hoping the transducers i've got work with it
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09:21 < Mokbortolan_> did that cheap tDCS guy ever come back?
09:21 < kanzure> nope
09:21 < kanzure> not really
09:21 < Mokbortolan_> shaaaady
09:22 < Mokbortolan_> I hope nobody actually gave him any money
09:22 < ThomasEgi> you guys still need that constant current source?
09:23 < Mokbortolan_> I'm still trying to find time to sort out my resistors, but I'm using the LM334
09:24 < Mokbortolan_> was looking at current monitors
09:25 < Mokbortolan_> thinking about v3, maybe with an LCD displaying the current
09:25 < ThomasEgi> why not get a cheap multimeter?
09:26 < Mokbortolan_> that's a thought
09:26 < Mokbortolan_> why reinvent the wheel, right?
09:26 < ThomasEgi> well. if the wheel is 100 times overpriced on the marked, there is reason to do so. but multimeters are pretty cheap, so..
09:31 < Mokbortolan_> ugh
09:31 < Mokbortolan_> all the cheap digital multimeters on amazon have complaints about drifting over tiem
09:33 < Mokbortolan_> or one five-star review :p
09:39 < kanzure> "PS: BPF just got our 501c3 application accepted last week. We will begin more active fundraising in a few weeks. Ken will be sending a Q1 Advisor Update email at the end of this month, he's already written most of it."
09:39 < kanzure> bpf=brain preservation foundation
09:39 < kanzure> apparently they have sebastien seung on their advisory board, so that's neat
09:39 < kanzure> i think that's john smart and ken hayworth but randal might have been pimping with them for a while
09:40 < Mokbortolan_> does formalin not work well?
09:41 < kanzure> iirc they had some chemical fixation complaints
09:42 < Mokbortolan_> what was it... a recent ampakine-based cognitive enhancer got scuttled and cortex pharm said it was the result of the fixative process used
09:43 < Mokbortolan_> during the analysis of the brain samples
09:43 < kanzure> scuttled?
09:43 < Mokbortolan_> a nautical term
09:43 < Mokbortolan_> when a boat is sunk intentionally
09:43 < ThomasEgi> Mokbortolan_, you really dont neet a terribly accurate multimeter. messuring 2 mA is something that's pretty easy, and a few percent drift wont really matterin this case.
09:44 < Mokbortolan_> they're resubmitting it for some other purpose
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09:58 < kanzure> isn't this the upverter guy? http://zakhomuth.com/sad-tired-and-alone-my-ongoing-battle-with-st-39237
09:59 < kanzure> maybe he feels bad that his product isn't open source (kidding)
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10:08 < Mokbortolan_> http://www.missingremote.com/guide/how-enable-concurrent-sessions-windows-7-service-pack-1-rtm
10:08 < Mokbortolan_> It works!
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11:10 < Steel2> Kanzure, what happened to the cure is now?
11:18 < kanzure> Steel2: i forget
11:18 < kanzure> something i'm sure
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11:28 < kanzure> "At the recent Global Future 2045 International Congress held in Moscow, 31-year-old media mogul Dmitry Itskov told attendees how he plans to create exactly that kind of immortality, first by creating a robot controlled by the human brain,"
11:28 < kanzure> "then by actually transplanting a human brain into a humanoid robot, and then by replacing the surgical transplant with a method for simply uploading a person’s consciousness into a surrogate ‘bot."
11:28 < kanzure> http://www.popsci.com/technology/article/2012-03/achieving-immortality-russian-mogul-wants-begin-putting-human-brains-robots-and-soon
11:31 < kanzure> oh shit why did i just link to a popsci article
11:31 < kanzure> forgive me
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12:30 < kanzure> google results are taking me >5sec to load these days
12:35 < chris_99> i wish they had an API for google scholar
12:36 < kanzure> webgl bipedal walking https://github.com/charlieschwabacher/Walking
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12:55 < ybit> kanzure: i don't think i've hired anyone
12:56 < Steel2> ybit, where do you work?
12:57 < ybit> it looks like marcin has handed over the initial research to apostol though
12:57 < ybit> Steel2: currently, i just attend school
12:58 < Steel2> ah
12:58 < ybit2> i guess you could say i work for kde right now
12:58 < ybit2> ;)
12:59 < Steel2> hah
12:59  * ybit2 just survived storm with tornadoes
12:59 < Steel2> where are you going to school?
12:59 < ybit2> and now i'm hungry
12:59 < ybit2> northwest shoals community college in muscle shoals, alabama
13:00 < ybit2> it will be my last semester there
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13:03 < Steel2> cool
13:03 < kanzure> ybit: apostol emailed me and said he's not doing anything and to ask someone else
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13:57 < kanzure> hi ParahSailin_
13:57 < ParahSailin_> howdy
13:57 < kanzure> fenn: https://github.com/mpictor/StepClassLibrary/wiki/python-generator
13:57 < kanzure> http://mpictor.github.com/scl/python/cd242/
14:04 < kanzure> monsanto data dump http://pastehtml.com/view/bpvygosbp.html
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14:32 < kanzure> boopity boop
14:33 < Juul> doo de doo
14:34 < kanzure> Juul: sup
14:35 < archels> kanzure: Would you work for Monsanto, or would you have ethical objections to it?
14:35 < Juul> kanzure, oh not much. trying to shuffle two years of data that's been kept in various spreadsheets and assorted file formats into a consistent database structure before the current BIOFAB shuts down
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14:38 < kanzure> archels: it would depend on what i'm doing
14:39 < kanzure> but no that's like asking "would you work for the federal government, or do you object to (say) the military"
14:41 < ThomasEgi> kanzure, easy answer: " GET OFF MY LAWN!!"
14:41 < kanzure> Juul: let me know if i can help
14:42 < Juul> kanzure, :)
14:42 < kanzure> Juul: one of my specialties is "yelling at you because your files are incomprehensible and your code sucks"
14:42 < Juul> kanzure, haha, the big problem was that they hired a guy with an MD to do their IT from the beginning
14:42 < kanzure> (or praising good stuff, but presumably you wouldn't need me to yell at you if it's good already)
14:43 < Juul> your code is bad and you should feel bad
14:44 < Juul> hm
14:46 < kanzure> Juul: see how motivating it can be?
14:46  * ybit hands a Juul a tissue
14:46 < Juul> :-/ it just makes me feel sad, since the people aren't trained in IT
14:47 < Juul> given that fact, i'm actually impressed by everything
14:47 < kanzure> Juul: how much stuff is there? what does the stuff cover
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14:49 < Juul> well i'm sorta in crunch mode now. ignoring everything except the final results: expression levels and reliability data for 5' UTRs, Promoters and Terminators. Then there's the sequences for these parts, their sub-parts and the plasmids.
14:49 < kanzure> new parts that aren't on partsregistry.org?
14:49 < Juul> yes
14:49 < kanzure> do they work
14:50 < kanzure> i mean, in a vaguely repeatable/known way
14:50 < Juul> the 5' UTRs are very good
14:50 < Juul> they'll be online by the end of this month
14:50 < kanzure> ah cool
14:51 < Juul> i'm making a little constraints-based search tool, where you can select the range of expression you're interested in and it will show results sorted by reliability. with some simple constraints to begin, like: ignore parts that have these restriction sites [list of sites]
14:51 < kanzure> 'range of expression'... expression levels?
14:53 < Juul> yeah, so we have promoters, 5' UTRs and terminators, and we've tested these in different combinations and with different genes. So we have some "score" for each of them that says something about how much these affect the amount of protein expressed. The expression level or we sometimes just refer to it as the part performance.
14:54 < Juul> Then we have the part reliability: How much performance varies when the part is composed with different parts. E.g. how much does a 5' UTRs translation level vary when used with different genes.
14:54 < kanzure> did you test this combinatorially to determine your score metric?
14:55 < Juul> yeah
14:55 < Juul> we have a bio-informatics guy who's been doing the modeling
14:55 < kanzure> lots of cell plates?
14:55 < Juul> yes lots and lots :-)
14:55 < kanzure> er i guess it could be lots of microarrays
14:55 < kanzure> i see
14:56 < Juul> i made an automated system that sucks in the .fcs files that the flow cytometer spits out, lets you associate them with plate layouts (defined previously via a web app), and then the rest is automatic
14:56 < kanzure> was plate loading a manual or automated procedure?
14:56 < Juul> it is analyzed using the BioConductor R libraries (flowCore and flowViz) and saved to the database.
14:56 < kanzure> neat
14:57 < kanzure> you should definitely publish your .fcs parsing code (i don't know what format that actually is, but i'm sure it's either csv or awful)
14:57 < Juul> the actual wet-lab side of things has been manual. we did look at automation, but we never really crossed the threshold where the time taken to set it up could be justified.
14:57 < kanzure> interesting, what was the setup time you estimated
14:58 < Juul> I'm using the flowCore R library from BioConductor to parse the fcs files. It isn't perfect, but it's better now that I found some bugs and submitted a patch.
14:58 < kanzure> and was that setup time w/ purchasing some commercial solution, or setup time for rolling your own equipment?
14:58 < kanzure> yay patches. ok. that makes me happy
14:59 < Juul> .fcs is a standardized file format. It's ugly, but at least there is a (sorta buggy) library to deal with it.
15:00 < archels> kanzure: Working for Monsanto might mean that your personal data is somewhere on that website right now. Does the next Joe PhD deserve that?
15:00 < kanzure> archels: my personal data is all over the web
15:00 < Juul> we have access to all of JBEIs automation, and experts in using the equipment. I think the decision was made because the wet-lab team felt like the time to learn how to use the equipment and to write and test the automation scripts might not pay off.
15:01 < kanzure> Juul: wow that's interesting
15:01 < kanzure> i would have thought it was something like "time to actually purchase/assemble/setup the equipment" not "training/our software" stuff
15:02 < Juul> yeah. that's something i wanted to look at more, but haven't had the time
15:03 < Juul> the workflow at the BIOFAB has been very ad-hoc
15:03 < Juul> which might be unexpected, since its stated goal is to make biology less of an ad-hoc process
15:04 < kanzure> most molecular biology labs are ridiculously ad hoc
15:04 < Juul> I think the team size and budget was just too small. If we'd been bigger we'd have had to develop a better process.
15:04 < Juul> kanzure, very true
15:04 < kanzure> to the point of "hey i just got done making a gel" -> "oh i made one hours ago for you it was sitting right there" -> "yeah i thought that was something else"
15:04 < Juul> according to what people tell me, Amyris is one of the least ad-hoc synth bio labs around.
15:04 < kanzure> Juul: what do you think of uh.. quartzy.com?
15:05 < kanzure> they do lab inventory SaaS crap
15:05 < archels> kanzure: Not everyone is like that you know. :P
15:05 < kanzure> archels: is your question about privacy or about whether or not i'd actually want to work at monsanto
15:05 < kanzure> :p
15:07 < archels> haha, mostly the latter
15:08 < kanzure> depends on how much money they are offering me.
15:16 < Juul> kanzure, it seems very simple. i'm sure it might be good for small labs with no IT staff. It seems like it's only marginally better than using google docs or a shared dropbox folder. In some ways it's worse. What BIOFAB needs is for their lab management system to be integrated with the workflow. If I'd had the time (and who knows, maybe the BIOFAB will actually continue and I'll still get the chance), the workflow would be something like: 0. Design p
15:16 < Juul> arts with whatever tool you have or by hand (these are short part) and feed them to the web app. 1. Plan experiment, design 96-well plate layouts. 2. Plan and simulate assembly using the web app. 3. Order parts. 4. Do assembly. 5. Send assembled parts for sequencing. 6. Feed received sequence files to web app for sequence checking. 7. Assuming no errors, go do your transformation with your assembled parts. 8. Shove the 96-well plate with your culture
15:16 < Juul> s into the flow cytometer and press the big green button. 9. Open up the web app and associate the new flow cyte results with the plate layout you made previously. 10. Rejoice! Performance and characterization data for your parts is now available through the nice web GUI..
15:17 < Juul> for now our assembly-tool is a third-party told and not integrated, and the sequence checker tool is in the web app but not fully integrated.
15:20 < Juul> it would make sense to expand this system with lab-management features, such that you could look up the protocols involved with all parts / strains and also find the location of any archived parts and strains.
15:20 < ParahSailin_> one does not simply *have* a flow cytometer
15:21 < Juul> well then i guess you'll have to put your 96-well plates on a flat-bed scanner and pretend it's a plate-reader :P
15:21 < Juul> we use the flow-cytometer because it gives better results, but we did use a plate-reader for some of the early experiments
15:22 < Juul> the third party software for the flow cytometer is a drag though
15:23 < ParahSailin_> id like to make a cheaper flow cytometer, maybe even a sorter
15:23 < kanzure> Juul: ah damn, plate layouts. is there a standard way to store that info or what
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15:26 < Juul> kanzure, it's possible. The simple thing to do would be use the SBOL core data model as the data structure for storing parts. Each strain is a part, containing sub-parts (promoter, 5' UTR, gene, terminator). Then just create a data structure that allows an arbitrary number of wells, each with a column and row and an associated Part of type Strain.
15:26 < kanzure> yeah lab workflows are a strange beast
15:26 < ParahSailin_> whats biofab
15:27 < Juul> ParahSailin, http://biofab.org/about
15:29 < Juul> One goal of the BIOFAB has been to make a set of Promoters, 5' UTRs and Terminators that are well-characterized, including how their function is affected when composed in different combinations. Another goal has been to design new parts in these categories that are more modular, i.e. their function varies less with context-changes.
15:29 < Juul> This has all been in E. coli so far.
15:29 < ParahSailin_> oh i think ive seen this
15:30 < Juul> I think Drew Endy is planning to work in yeast as well.
15:33 < Juul> To summarize results: Promoters and 5' UTRs can be composed without completely changing the function of either. 5' UTRs and genes cannot. Terminators can also be composed fairly reliably. Mutalik et al. (of BIOFAB) has designed and tested 5' UTRs that are more modular, based on previous research into highly-expressing problematic proteins.
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15:33 < Juul> two papers are in the pipeline
15:37 < kanzure> your step 4 (assembly) is assembly into the plasmid?
15:38 < kanzure> i guess not, you have no reason to resequence plasmids
15:38 < kanzure> prolly just ligating your promoters and other parts
15:41 < kanzure> Juul: so i guess once you've defined the workflow, you don't really change it
15:42 < kanzure> my time spent in molecular biology labs has been mostly undocumented workflows other than some scribblings in a notebook sometimes
15:42 < kanzure> never ever has it been "Here's a specific stack of documents about this particular workflow"
15:42 < kanzure> but i'm p. sure it's like that in companies (or, i would hope)
15:45 < strangewarp> So I found a nootropic drink in the organic food store, featuring citicoline
15:45 < strangewarp> has anyone else had experience with citicoline? I'm noticing a profound benefit after just a couple hours
15:45 < Mokbortolan_> really
15:46 < Mokbortolan_> I read that citicholine is awesome on every site that sells it :p
15:46 < Mokbortolan_> so I've been sort of on the fence about trying it
15:46 < strangewarp> I've been meaning to buy piracetam supplements but I'm currently an unemployed mooch.. citicoline seems pretty good but I don't have experience with anything else
15:47 < kanzure> el neato http://blog.stackoverflow.com/2011/09/creative-commons-data-dump-sep-11/
15:47 < Mokbortolan_> I run a piracetam store, my prices are very low
15:47 < strangewarp> o rly !
15:47 < strangewarp> throw me a link, I may be a future customer then
15:48 < Mokbortolan_> I've got a subreddit with a few folks who can confirm that I'm not a scammer
15:48 < strangewarp> hmm, good good
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15:49 < kanzure> Mokbortolan_: nah you might be a scammer, but you scam good shit
15:49 < Mokbortolan_> :p
15:50 < Mokbortolan_> I'm too scrupulous to be a scammer
15:50 < Juul> kanzure, yes to the ligating. and yeah, the biofab has a pretty stable workflow, and not all labs have that, but i think the whole "design -> construct -> verify -> implement -> analyze results" pipeline is, or at least will be, shared between many synth-bio groups. they will need different code modules to use different assembly methods and analyze different results
15:50 -!- joshcryer [~g@unaffiliated/joshcryer] has joined ##hplusroadmap
15:50 < joshcryer> http://bcove.me/nz28d1ph
15:50 < Mokbortolan_> besides, reddit will come down on you like a ton of bacon for messing around
15:50 < joshcryer> http://iopscience.iop.org/1367-2630/14/3/033001/article
15:51 < Juul> woah, new respect for stackoverflow
15:51 < Mokbortolan_> and that's where most of my customers come from, so I don't mess around
15:51 < Mokbortolan_> the worse I do is ship late because I have a busy life
15:51 < Mokbortolan_> worst
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15:52 < strangewarp> hmmmm
15:52  * strangewarp adds that nootropics site to bookmarks
15:53 < Mokbortolan_> besides, I have ~3000 comment karma, I'd hate to lose it! :p
15:53 < Juul> joshcryer, isn't that info lost when the radio signals bounce off matter?
15:56 < kanzure> Juul: who's been doing the synthesis work for biofab?
15:56 < joshcryer> Juul, not sure, I am only halfway through the paper.
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15:56 < Juul> kanzure, IDT
15:56 < Juul> joshcryer, ok, interesting though.
15:57 < kanzure> Juul: what's the terms? $0.20/bp? 7-day turn around?
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15:58 < Juul> kanzure, hm, not sure, pretty sure it's faster than that. we have only needed short oligo synthesis, since the parts we deal with don't require anything more
15:58 < kanzure> well idt has their "overnight delivery" option but iirc that's not their standard offer
15:58 < joshcryer> Juul, even still, it has uses through OTA and space based communications. Effectively infinite bandwidth (limited only by your ability to build transmitters).
15:59 < Juul> joshcryer, yes true, but if it works in urban settings it would have a lot of real-world impact "now"
15:59 < Juul> well, i gotta go pick up a cyberanthropologist at the airport now
15:59 < Juul> bbl
15:59 < kanzure> seeya
15:59 < joshcryer> Later.
16:00 < kanzure> god damn cyberapologists
16:00 < Urchin> cyberanthropologists?
16:01 -!- augur [~augur@129.2.129.33] has quit [Ping timeout: 244 seconds]
16:01 < Urchin> never mind, not rational right now
16:02 < foucist> none of those exist.. this ain't a cyberpunk world
16:02 < joshcryer> kanzure, may I ask, and forgive me if I'm overstepping, but why do you seem to be focused on bio so much? I see a lot of jargon that is just over my head. Not that I'm against it, if that's your niche go for it, etc.
16:03 < kanzure> joshcryer: because none of you in here seem to be able to help me with the CAD/engineering stuff
16:04 < kanzure> hmm that's probably not the answer you want
16:04 < joshcryer> That's fair enough in any case. If bio is popular then so be it.
16:04 < kanzure> there's a lot of low-hanging biohacking fruit that directly or nearly-directly contributes to human improvements
16:05 < joshcryer> Such as age lengthing? Cure for cancer?
16:05 < kanzure> also if you don't understand the jargon, just ask a naseating number of questions
16:05 < kanzure> aging is still a tricky one http://diyhpl.us/~bryan/papers2/longevity/
16:05 < kanzure> cancer has tons of options available for sure
16:06 < joshcryer> I do lots of engineering work in my daily life so I think it would be silly of me to try a different field. We'll do the CAD/engineering stuff in due course, when I have more free time.
16:07 < kanzure> wait why is it stilly of you to try something else?
16:07 < kanzure> when engineers have stuck their head into biology, even just a little bit, a lot of cool things have happened
16:08 < joshcryer> I have never been able to get a hang of bio, it's hard stuff. I read the logs and my eyes gloss over. :P
16:08  * joshcryer afks to walk the dog
16:09 < kanzure> that's probably because you don't ask about it?
16:12 < Mokbortolan_> sometimes I try to imagine the insane chemical riot that goes on inside a human body
16:13 < Mokbortolan_> and if I focus on it long enough, I get a very strange lightheadedness before I have to stop
16:13 < kanzure> that's just called lsd
16:13 < Mokbortolan_> I mean, what's going on in just a single drop of blood
16:14 < Mokbortolan_> hormones, waste products, oxygen, lymphocytes, hematocytes, intrinsic factors, environmental contaminants, carbon dioxide, platelets, antibodies
16:15 < Mokbortolan_> heck, even what goes on inside a single cell
16:15 < Mokbortolan_> not to mention the insanely complex interplay
16:16 < kanzure> i should introduce you to an immune system textbook
16:16 < kanzure> you'll either laugh or murder me
16:16 < Mokbortolan_> once we can electronically expand working memory, perhaps we'll be able to better understand things
16:17 < ThomasEgi> i dont think memory is a limited recource within the brain
16:17 < Mokbortolan_> working memory certainly is
16:18 < kanzure> aww i can't find a good diagram of the wound healing process
16:18 < kanzure> anyway there's like 40 enzymes that are known to directly impact the scarring process
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16:22  * Mokbortolan_ imagines cells rolling along like fat soggy deflated beachballs.
16:23 < Mokbortolan_> does prosaposin affect wound healing?
16:23 < Mokbortolan_> wait, wrong protein
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16:27 < Mokbortolan_> I remember reading about a drug that inhibits the protein involved in cell movement
16:28 < Mokbortolan_> and I wondered why it wasn't a silver-bullet to stop metastasis, then realized cells probably need to move normally
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16:42 < joshcryer> I'm not sure bio has very much to contribute toward "clean water, nutritious food, affordable housing, personalized education, and non-polluting, ubiquitous energy."
16:43 < Mokbortolan_> why not?
16:43 < Mokbortolan_> GMO algae, for one
16:43 < joshcryer> Useful for archaic combustion engine technology, sure.
16:44 < Mokbortolan_> or fuel cells
16:45 < Mokbortolan_> there are some fuel cells that can use hydrocarbons
16:45 < joshcryer> DEFCs do have some promise, I admit.
16:45 < Mokbortolan_> also, understanding the mechanisms already in use by the natural world can inform other sciences
16:46 < Mokbortolan_> but at the end of the day, if you don't have a passion for it, I suggest you find your passion :p
16:46 < Mokbortolan_> 'cos that's where you'll be most useful in creating part of your goal
16:47 < joshcryer> Replicators it is. ;P
16:47 < Mokbortolan_> technically though
16:48 < Mokbortolan_> there are replicators that can turn low-value cellulose into high-quality proteins :p
16:48 < joshcryer> Yeah, they make inexact copies, and some are highly flawed and don't survive their environment for long.
16:49 < joshcryer> I'm in the mind of Lackner-Wendt Auxon's, hive replication. Large industrial factories that can make anything with the right stocks.
16:49 < joshcryer> I do think labmeat is a useful use of bio though.
16:50 < Mokbortolan_> oh
16:50 < Mokbortolan_> I was referring to goats
16:52 < Steel_> I'm going to buy exclusively lab grown meat when I can
16:52 < Steel_> also, goats are delicious
16:53 < joshcryer> Same here, Steel_.
16:53 < Mokbortolan_> I like the idea of quorn
16:54 < joshcryer> I know a lot of vegetarians who will, too.
16:54 < Mokbortolan_> what's wrong with mycoprotein?
16:54 < Mokbortolan_> it actually tastes pretty good, too
16:54 < joshcryer> I love mushrooms. :P
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16:55 < Mokbortolan_> it's not a mushroom
16:55 < Mokbortolan_> it's closer to a mold
16:55 < Mokbortolan_> they engineered the toxins out of it
16:56 < Mokbortolan_> Fusarium venenatum
16:56 < joshcryer> Hmm, where can I get it?
16:56 < Mokbortolan_> health food store, in the vegetarian section
16:56 < Mokbortolan_> frozen
16:56 < Mokbortolan_> it's not bad, IMO
16:57 < Mokbortolan_> though, technically the product you buy isn't pure mycoprotein, they add egg white as a binder and texturizer
17:02 < joshcryer> Looks like flaxseed could be a useful replacement for egg whites.
17:03 < joshcryer> I grew up on a farm, farm animals are a pain. Until you eat them. Then it's almost worth it.
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17:04 < Mokbortolan_> it's easier to just cultivate wild animasl
17:04 < Mokbortolan_> animals
17:05 < joshcryer> Nah, domesticated animals are cool, they come to you not knowing you're going to eat them.
17:06 < joshcryer> Wild animals are always suspecting that you will eat them. :P
17:08 < Mokbortolan_> well that's what makes it fun to hunt them down
17:08 < Mokbortolan_> ref: precolonial America
17:09 < joshcryer> Yeah but hunting isn't easy!
17:09 < Mokbortolan_> it's good exercise
17:09 < joshcryer> Out of a 4 day hunt we only caught one buck when I was a kid. I thought my neighbors were crazy. But, effective. We were poor so one 20 cent bullet fed a family of 6 for a winter.
17:09 < Mokbortolan_> makes it tough to develop an industrial society if you're either hunting or picking berries, though
17:10 < Mokbortolan_> joshcryer: if that was your only protein source I'll bet you'd get better at it :p
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17:11 < strangewarp> I want to put the future in my mouth
17:11 < strangewarp> 0_0
17:12 < Mokbortolan_> taste the rainbow?
17:12 < joshcryer> Eat some memristors.
17:12 < n_bentha> who said hunting isn't easy?
17:13 < joshcryer> There was some recent drama on memristors: http://www.newscientist.com/article/mg21328535.200-online-spat-over-who-joins-memristor-club.html
17:14 < joshcryer> n_bentha, I said that from my personal experience, standing out in the woods for 4 days straight is not easy, when you can slaughter a cow.
17:14 < Mokbortolan_> I read there was some recent movement in the commercial world
17:16 < n_bentha> True, josh, but I'd rather go hunting.
17:16 -!- Juul [~Juul@slim.dhcp.lbl.gov] has quit [Ping timeout: 252 seconds]
17:16 < n_bentha> But you do have a point. 4 days is a little much.
17:18 < joshcryer> n_bentha, I was a teenage city slicker, after we were done I was appreciative of it. They may have been testing me in retrospect. Haven't gone since, but I'm not opposed to it or anything.
17:18 < joshcryer> And dang, I didn't know John McCarthy died.
17:18 < kanzure> i just had the weirdest call with sebastien seung
17:19 < kanzure> couldn't understand a word he was saying
17:19 < kanzure> but he sounded disappointed in me
17:19 < kanzure> oops
17:19 < kanzure> not sebastien seung
17:19 < kanzure> sebastien someone-else from longecity
17:20 < joshcryer> Who could be disappointed in you? :(
17:30 < joshcryer> Did you do something to Longecity? :P
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18:12 < kanzure> hi yashgaroth
18:12 < yashgaroth> hey
18:12 < yashgaroth> the diybio discussion is somewhat more productive than the transhumani one, I must say
18:13 < kanzure> and what sucks is that you and i both know diybio could be way better
18:14 < yashgaroth> they've gotta move out of 'talking about e.coli' some day...not that there's anything wrong with bacteria, but seriously
18:15 < kanzure> genspace does some tissue culture stuff
18:16 < yashgaroth> too bad there's no biotech in NYC to keep me employed
18:16 < kanzure> but to be honest ever since they stopped calling themselves diybio-nyc none of them are regular contributors to the diybio group
18:16 < kanzure> they were really hostile against knowing me for instance, one of them went as far as saying she only talked with people over the net that she personally knows
18:16 < kanzure> (wtf?)
18:16 < yashgaroth> hahaha
18:19 -!- strages_2600 [~strages@256.makerslocal.org] has quit [Ping timeout: 260 seconds]
18:19 < yashgaroth> still, it went better than I expected
18:21 < yashgaroth> also if I may, regarding 16:42 < joshcryer> I'm not sure bio has very much to contribute toward "clean water, nutritious food, affordable housing, personalized education, and non-polluting, ubiquitous energy."
18:21 < kanzure> heh "nutritious food"
18:21 < kanzure> (well especially food)
18:21 < yashgaroth> plants can take the dirtiest water imaginable and turn it into pure water, you just gotta make them have it accessible
18:21 < yashgaroth> nutritious food, that one's too easy
18:22 < yashgaroth> housing, trees are biological
18:22 < yashgaroth> education...um, skip that one
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18:22 < yashgaroth> energy, GMO algae etc don't release any net CO2; it doesn't matter how much gas you guzzle, all the CO2 goes back into the algae and converted
18:23 < yashgaroth> not to mention heavily modifying plants to output DC current
18:24 < yashgaroth> also, hydrocarbons are extremely energy-dense, far more so than any potential battery
18:24 < yashgaroth> ok I'm done
18:26 < yashgaroth> the only useful part of lab-grown meat is the ability to eat human burgers
18:29 < strangewarp> Hmm
18:29 < strangewarp> https://www.destroyallsoftware.com/talks/wat - Was just linked this video; I figure it has some cross-appeal here, since it's comedy about some code
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18:32 < kanzure> strangewarp: seen it :)
18:32 < strangewarp> yay \o/
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18:39 < Vicarious> hi
18:42 < sylph_mako> kanzure do your thing.
18:44 < sylph_mako> fine then.
18:44 < sylph_mako> Hell Vicarious, what brings you here?
18:44 < sylph_mako> hello*
18:45 < Vicarious> oh I just read some e-mails on the hackerspaces.org mailing list which pointed me here
18:46 < kanzure> hi Vicarious
18:46 < Vicarious> hello
18:47 < kanzure> welcome, i guess you like hackerspaces then
18:47 -!- zacharycohn [~zacharyco@c-98-247-247-157.hsd1.wa.comcast.net] has joined ##hplusroadmap
18:47 < Vicarious> in fact, I am in our hackerspace right now \o/
18:47 < kanzure> biocurious?
18:47 < Vicarious> but going home soon, it's 3:47 a.m. and everybody else already left
18:49 < Vicarious> I watched lepht anonym's awesome lecture at 27C3 from the basement of the bcc, that got me interested in transhumanism
18:49 < Vicarious> so far I only implanted a magnet under the skin of my left hand.. couldn't get it in the fingertip
18:50 < Vicarious> pics or it didn't happen: http://www.flickr.com/photos/ivicarious/6492287455/
18:50 < kanzure> no i believe you
18:51 < kanzure> what sort of hackerspace stuff do you do? biotech? machining? electronics? softwaring?
18:53 < sylph_mako> Vicarious, so.. how well does that work relative to putting the thing in your fingertip?
18:53 < Vicarious> sylph_mako: good question, I don't have one in my fingertip yet, that's still on my to do list
18:54 < Vicarious> kanzure: I do different stuff.. mostly hardware hacking
18:55 < Vicarious> I'm one of the founders of our hackerspace, recently we moved to a new location where we have 24/7 access
18:56 < kanzure> so.. lab hardware? electronics? christmas lights? :P
18:57 < Vicarious> some electronics, no christmas lights but I made a christmas tree from cardboard and 13 leds and arduino uno
18:58 < Vicarious> https://hackerspaces.nl/wp-content/uploads/2011/12/foto.jpg
18:58 < Vicarious> and made a lamp from an old empty macintosh se/30 case
18:59 < kanzure> Vicarious: do you know pieter van boheeman
18:59 < Vicarious> and I do some lockpicking, one of the few who maintain the network infrastructure of the building, etc
18:59 < kanzure> or jelmer cnossen
18:59 < kanzure> or koen martens
18:59 < Vicarious> kanzure: no, don't know either of those
18:59 < Vicarious> I know koen
18:59 < Vicarious> aka gmc
18:59 < kanzure> hrm well close enough i guess
19:00 < Vicarious> he's from RevSpace, hackerspace in The Hague
19:00 < kanzure> pieter is running around the internet trying to organize a do-it-yourself biohacking event in tandem with open science summit 2012
19:00 < kanzure> with joseph jackson
19:00 < Vicarious> ok
19:00 < kanzure> anyway, i just remembered that pieter is in your area so maybe he goes to your hackerspace
19:01 < Vicarious> our hackerspace is in the very far south of .nl
19:01 < Vicarious> heerlen
19:01 < Vicarious> looks like pieter is from the hague
19:01 < joshcryer> What kind of biohacking can you show off?
19:01 < kanzure> i know nothing of yuor geography
19:02 < kanzure> *your
19:02 < kanzure> joshcryer: what?
19:04 < Vicarious> sylph_mako: btw, having a magnet in the back of the hand does have an advantage.. last year at Chaos Communication Camp conference, I was making some throwies (led, battery and neodymium magnet wrapped in tape) and attached one throwie to my hand
19:06 < joshcryer> "do-it-yourself biohacking event"
19:06 < Vicarious> it was useful at night, had both hands available, didn't have to carry a flashlight while I climbed in my tent or when I went to the toilet, etc
19:06 < joshcryer> What does one do at events but show off stuff?
19:06 < kanzure> joshcryer: give tutorials, present results, poster sessions, brainstorming, microscope show-and-tell, trade petri dishes..
19:07 < kanzure> impromptu hardware plug-and-play stuff
19:12 < Vicarious> really going home now :)
19:15 < ParahSailin_> you put a magnet in your hand?
19:16 < bkero> Where'd you source the magnet?
19:16 < bkero> who'd you get to inject it and in which finger?
19:16 < sylph_mako> not finger
19:16 < Vicarious> who? me?
19:22 < bkero> oh back of hand
19:22 < bkero> I need to learn to read the back buffer
19:22 < Vicarious> yes, did you see the url? :)
19:24 < bkero> nope
19:24 < Vicarious> ok
19:25 < ParahSailin_> you should get that mole looked at
19:25 < bkero> dude that subdermal didn't go very well
19:26 < Vicarious> that's where the magnet is, probably didn't inserted it deep enough
19:27 < Vicarious> Did it myself, piercing/tattoo studio wouldn't do it
19:27 < bkero> yeah
19:27 < Vicarious> I tried to put it in my fingertip, but failed
19:28 < bkero> That's where it's supposed to go
19:28 < bkero> but you need to put it at the corner of the tip and the pad
19:28 < Vicarious> I know
19:28 < bkero> from slightly on the pad side
19:28 < Vicarious> Didn't have a piercers needle or scalpel
19:35 < bkero> that shit is important enough to wait and get the proper tools
19:36 < Vicarious> meh, I sterilized everything, wound didn't get infected, everything is fine
19:39 < bkero> sure
19:39 < bkero> but it was a failed placement
19:40 < yashgaroth> how long after the implantation was that picture taken? does it look less inflamed now?
19:40 < yashgaroth> sorry to keep you up :/
19:42 < joshcryer> are you lepht?
19:43 < Vicarious> I implanted the magnet early july last year, so that the wound would be healed before Chaos Communication Camp 2011
19:44 < bkero> Vicarious: were you at fosdem this year?
19:45 < yashgaroth> josh: lepht is british and female so I doubt it
19:47 < joshcryer> yashgaroth, darn.
19:47 < yashgaroth> I don't think she comes in here much
19:47 < Vicarious> I think the photo mentions when it was taken, it still looks the same as in the photo
19:48 < joshcryer> Vicarious, I have a nice deep scar on the back of my hand.
19:48 < joshcryer> From... removing a transmission in a car.
19:49 < Vicarious> ok
19:49 < bkero> those happen
19:50 < bkero> I've done that twice.  Both times they were transversely mounted FWD style, and I had to literally get under the car, hug the transmission, and get someone to pull me out from under the car
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19:51 < Vicarious> just got home..
19:51 < joshcryer> gore kinda: http://i52.tinypic.com/2klbf5.jpg
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19:52 < sylph_mako> Personally I'm reluctant to let go of the property of being entirely magnetically inert. I just think it's neat. You're not gonna get another chance like this in your transhuman life.
19:52 < sylph_mako> I'm going to miss running naked through EMR rooms.
19:53 < Vicarious> bkero: I ordered the minimum amount of 20 magnets from supermagnete.nl: http://www.supermagnete.nl/eng/S-02-01-N
19:53 < Vicarious> and ordered a package of sugru
19:54 < bkero> oh christ
19:54 < yashgaroth> I believe people on biohack still have some of the parylene-coated magnets from the group buy
19:54 < bkero> You'r enot telling me you have sugru embedded beneath your skin
19:55 < kanzure> bkero: someone was popularizing using sugru
19:55 < bkero> kanzure: is the composition of sugru stable?  Is it going to fuck with some biochemical pathways?
19:55 < bkero> more than something like silicon?
19:55 < bkero> *silicone
19:55 < Vicarious> couldn't find where I could order 7mm hollow piercers needles from, so I used a sharp knife instead.. I thought it would be as good as a scalpel, but I'm a noob
19:56 < Vicarious> lepht suggested either sugru or hot glue in her lecture on 27C3
19:57 < Vicarious> as bioproof coating material
19:58 < Vicarious> magnet coated in sugru has been under my skin for 8 months now, haven't experienced any problems so far
20:00 < Vicarious> even though it's not in the fingertip where it's supposed to be, I can still feel the power supply of my laptop when it gets near the magnet
20:00 < Vicarious> or another magnet when it gets near
20:04 < Vicarious> and no, I haven't attended fosdem
20:06 < Vicarious> in a couple hours I'm attending the opening party of another hackerspace in the netherlands, going to take a nap now
20:08 < Vicarious> goodnight
20:22 < vrs> yashgaroth: yep, I have 20 here
20:22 < vrs> haven't implanted one yet, but worn one attached  to my finger with surgical tape
20:23 < vrs> bkero: hm well, you need to ask people like lepht who use sugru coating and not parylene coating
20:23 < vrs> but as far as I know, it's pretty bioproof
20:23 < yashgaroth> hey vrs can you send me a few? I'll give you monies
20:24 < vrs> I haven't been to biohack in a while, do they have a second group buy running?
20:24 < vrs> Vicarious: sovereignbleak did a video about his install procedure
20:24 < yashgaroth> no idea, though the company they used last time is down the street from me
20:24 < vrs> lepht did too, but it was on megavideo...
20:25 < vrs> yashgaroth: nice
20:25 < vrs> wait lemme dig it up
20:25 < vrs> http://vimeo.com/23836862
20:25 < yashgaroth> I've been thinking about trying the tape; if it survives the magnetic stir plates I work with every day, I'll probably get an implant
20:25 < vrs> tape is definitely the way to test
20:26 < vrs> what I experienced after a few days was that I could sense magnetic materials and static fields from a few mm to cm
20:26 < vrs> implants give you more the dynamic type
20:27 < vrs> (I heard)
20:27 < yashgaroth> I'd imagine so, especially if you get a nerve close by
20:28 < vrs> I put the procedure off due to lack of money so far, and I don't know if I'm hardcore enough for DIY
20:29 < yashgaroth> no way I'm trusting myself with that, I'll probably head to AZ and have haworth do it if he's still active
20:29 < vrs> you shouldn't do it entirely yourself anyway
20:29 < vrs> have a friend help you or something
20:30 < yashgaroth> someone who isn't fumbling with a scalpel as they bleed out
20:30 < vrs> exactly
20:30 < yashgaroth> too bad I never befriended any pre-meds in school
20:31 < Vicarious> vrs: I've seen those videos.. I used icewater to numb my finger, sharp knife instead of piercers needle or scalpel
20:31 < vrs> how did it work out?
20:32 < vrs> mh reading backlog
20:32 < vrs> you'd need a *very* sharp knife
20:32 < Vicarious> items from a first aid kit I had at home to sterilize the knife and skin and magnet with sugru coating
20:33 < vrs> sterilize everything
20:33 < Vicarious> I did
20:33 < vrs> good
20:33 < Vicarious> no infections
20:33 < Vicarious> wound healed fine as expected
20:33 < vrs> I might just try that in some less visible area too
20:37 < yashgaroth> vicarious: did you use stitches or superglue or something to close it?
20:37 < Vicarious> I follow a first aid / fire safety / evacuation course every year at the local fire department, so I know some basics about sterilization and bandages and bandaids ;)
20:40 < Vicarious> yashgaroth: it was a small incision, so I used a sterile dressing pad and bandage from the same first aid kit
20:41 < Vicarious> replaced the dressing pad daily with a new one
20:41 < yashgaroth> I ask because you don't seem to have any scarring, which is impressive
20:42 < Vicarious> later I replaced them with a smaller adhesive dressing pad and after that regular bandaids
20:44 < Vicarious> anyway, nap ;)
20:44 < yashgaroth> yes, sleep
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21:02 < ParahSailin_> id like someone to help me take a dermal biopsy for fibroblasts
21:02 < yashgaroth> your fibroblasts?
21:02 < ParahSailin_> hells yeah
21:03 < yashgaroth> planning on needing a skin transplant?
21:03 < ParahSailin_> no i just wanna make some ips cells
21:03 < ParahSailin_> chill em in nitrogen until i need them
21:04 < yashgaroth> you're gonna need some MEF cells too, if they still use those for the protocol
21:06 < ParahSailin_> no, people can do them with just autologous fibroblasts
21:07 < yashgaroth> I'll admit I haven't been keeping up on ESC culturing methods
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22:16 < kanzure> grr yaml still does not do ordered dictionaries
22:19 < joshcryer> Will !!omap work?
22:27 < kanzure> ConstructorError: while constructing an ordered map
22:27 < kanzure> expected a sequence, but found mapping in "<string>", line 1, column 1: !!omap
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22:29 < kanzure> "!!omap\n- 123: hi\n- 123A: yepr\n- '0047': noooo"
22:29 < kanzure> this seriously defeats the purpose of readability
22:29 < kanzure> so now all of my dictionaries look like lists
22:30 < joshcryer> http://stackoverflow.com/questions/5121931/in-python-how-can-you-load-yaml-mappings-as-ordereddicts
22:31 < kanzure> yes i know how to use google
22:31 < kanzure> their ticket hasn't been closed for three years
22:31 < kanzure> this gives me the right to complain
22:32 < joshcryer> Did you try what that guy "came up with" which he claims "does work"?
22:33 < kanzure> that's a monkeypatch man
22:35 < kanzure> bleh
22:35 < kanzure> fine
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22:39 < joshcryer> (For what it's worth I don't care about complaining or anything like that, I was just trying to be helpful.)
22:40 < kanzure> yaml.load("a: hi\nb: yep\nc: no\n1: hooooray", OrderedDictYAMLLoader)
22:40 < kanzure> OrderedDict([('a', 'hi'), ('b', 'yep'), ('c', False), (1, 'hooooray')])
22:40 < kanzure> yaml.dump(OrderedDict([('a', 'hi'), ('b', 'yep'), ('c', False), (1, 'hooooray')]))
22:40 < kanzure> '!!python/object/apply:ordereddict.OrderedDict\n- - - a\n    - hi\n  - - b\n    - yep\n  - - c\n    - false\n  - - 1\n    - hooooray\n'
22:40 < kanzure> that's not very close to the original input
22:41 < kanzure> even when i set default_flow_style=False
22:41 < joshcryer> Try json.dumps ?
22:41 < kanzure> json is not yaml
22:42 < kanzure> i don't want json
22:42 < joshcryer> json is yaml, yaml is not json, technically.
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22:43 < kanzure> json syntax is a subset of yaml syntax, yes
22:43 < kanzure> anyway, no i don't want json
22:44 < joshcryer> Just try it man, you can always convert json to yaml. Something is broke, work around it. :P
22:44 < kanzure> yes, i use json all the time
22:44 < kanzure> the whole point of using yaml is the pretty formatting which json lacks
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23:16 < joshcryer> kanzure, I think you'll find if you put that text in a variable and dump and load it the result will be the same...
23:17 < joshcryer> !!python/object/apply:ordereddict.OrderedDict
23:17 < joshcryer> - - - a
23:17 < joshcryer>     - hi
23:17 < joshcryer>   - - b
23:17 < joshcryer>     - yep
23:17 < joshcryer>   - - c
23:17 < joshcryer>     - false
23:17 < joshcryer>   - - 1
23:17 < joshcryer>     - hooooray
23:18 < kanzure> yeah but that's not how i want my text formatted at all
23:18 < kanzure> notice that - - 1 is a list of a list
23:18 < sylph_mako> You people call yourselves transhumanists. Use a binary serialization format with a viewing augmentation!
23:18 < kanzure> even though the !! identifier will force it to be loaded as an OrderedDict in python2.6
23:18 < sylph_mako> Admittedly there are no viewing augmentations.
23:18 < sylph_mako> I'm working on it.
23:21 < joshcryer> kanzure, you want this:
23:21 < joshcryer> !!python/object/apply:collections.OrderedDict
23:21 < joshcryer> - - [a, hi]
23:21 < joshcryer>   - [1, hooooray]
23:21 < joshcryer>   - [c, false]
23:21 < joshcryer>   - [b, yep]
23:21 < joshcryer> ?
23:22 < kanzure> i want this:
23:22 < kanzure> a: hi
23:22 < kanzure> b: yep
23:22 < kanzure> c: false
23:22 < kanzure> this is not hard :(
23:23 < joshcryer> I blame PyYAML.
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--- Log closed Sat Mar 03 00:00:35 2012